The algorithm used by dot (Sugiyama layout) works well for trees or any other graph where the structure is well-approximated by a tree. Control-flow graphs are the prototypical example of the latter (being the use case dot was explicitly designed for), but the VCS commit graph is also going to fit in well in this model. If you have a graph which has many more cycles in it, or has a crisscrossing connectivity pattern like a hypercube, the resulting layout from dot is going to be a giant ball of twine.
Most demos i've seen on JS libraries have been laggy with just a handful of nodes - but they're also trying to do fancy animations/etc by default. Hopefully i can hook up D3 with some minimal effort - or perhaps render it in a game library. /shrug
Old me would have been able to do this in LaTeX.
Ultimately i think i just want to find a decent way to use CSS to replicate this style - but i've not seen any CSS gurus manage to produce that.
Though, WebGL might be the best way regardless.